DiffractionData object for Single Crystal analysis. More...

Inheritance diagram for ObjCryst::DiffractionDataSingleCrystal:

Collaboration diagram for ObjCryst::DiffractionDataSingleCrystal:

Public Member Functions
	DiffractionDataSingleCrystal (const bool regist=true)
	Default constructor. More...

	DiffractionDataSingleCrystal (Crystal &cryst, const bool regist=true)
	Constructor, with an assigned crystal structure. More...

	DiffractionDataSingleCrystal (const DiffractionDataSingleCrystal &old)
	Copy constructor.

virtual DiffractionDataSingleCrystal *	CreateCopy () const
	So-called virtual copy constructor.

virtual const string &	GetClassName () const
	Name for this class ("RefinableObj", "Crystal",...). More...

const CrystVector_REAL &	GetIcalc () const
	returns the calculated diffracted intensity. More...

std::map< RefinablePar *, CrystVector_REAL > &	GetIcalc_FullDeriv (std::set< RefinablePar * > &vPar)

const CrystVector_REAL &	GetIobs () const
	Return the array of observed intensities for all peaks.

void	SetIobs (const CrystVector_REAL &)
	Return the array of observed intensities for all peaks.

const CrystVector_REAL &	GetSigma () const
	Return the array of sigmas for observed intensities, for all peaks.

void	SetSigma (const CrystVector_REAL &)
	Return the array of sigmas for observed intensities, for all peaks.

void	SetIobsToIcalc ()
	Set Iobs to current values of Icalc. Mostly used for tests.

const CrystVector_REAL &	GetWeight () const
	Return the weights (for each reflection) used for computing Rw.

void	SetWeight (const CrystVector_REAL &)
	Change the weights (for each reflection) used for computing Rw.

void	SetHklIobs (const CrystVector_long &h, const CrystVector_long &k, const CrystVector_long &l, const CrystVector_REAL &iObs, const CrystVector_REAL &sigma)
	input H,K,L, Iobs and Sigma More...

void	ImportHklIobs (const string &fileName, const long nbRefl, const int skipLines=0)
	Import h,k,l,I from a file. More...

void	ImportHklIobsSigma (const string &fileName, const long nbRefl, const int skipLines=0)
	Import h,k,l,I,Sigma from a file. More...

void	ImportShelxHKLF4 (const string &fileName)
	Import h,k,l,I,Sigma from a file using shelx HKLF 4 format. More...

void	ImportCIF (const string &fileName)
	Import diffraction data from a CIF file. More...

void	ImportHklIobsSigmaJanaM91 (const string &fileName)
	Import h,k,l,I,Sigma from a Jana98 '*.m91' file. More...

void	ImportHklIobsGroup (const string &fileName, const unsigned int skipLines=0)
	Import h,k,l and grouped intensities from a file. More...

virtual REAL	GetRw () const
	Return the Crystal R-factor (weighted) More...

virtual REAL	GetR () const
	Return the Crystal R-factor (unweighted) More...

virtual REAL	GetChi2 () const
	Return conventionnal Chi^2. More...

virtual void	FitScaleFactorForRw () const
	Compute the best scale factor minimising Rw. More...

virtual void	FitScaleFactorForR () const
	Compute the best scale factor minimising R. More...

virtual REAL	GetBestRFactor () const
	Compute the best scale factor to minimize R, apply this scale factor and return the R value obtained. More...

virtual void	SetSigmaToSqrtIobs ()
	Set sigma for all observed intensities to sqrt(obs) More...

virtual void	SetWeightToInvSigma2 (const REAL minRelatSigma=1e-4, const REAL minIobsSigmaRatio=0)
	Set the weight for all observed intensities to 1/sigma^2. More...

REAL	GetScaleFactor () const
	Scale factor (applied to Icalc to match Iobs)

virtual void	PrintObsData () const
	Print H, K, L Iobs sigma for all reflections. More...

virtual void	PrintObsCalcData () const
	Print H, K, L Iobs sigma Icalc for all reflections Iobs and sigma (if given) are scaled to Icalc (if available).

virtual void	SetUseOnlyLowAngleData (const bool useOnlyLowAngle, const REAL angle=0.)

void	SaveHKLIobsIcalc (const string &filename="hklIobsIcalc.out")
	Save H,K,L Iobs Icalc to a file, text format, 3 columns theta Iobs Icalc. More...

virtual void	GlobalOptRandomMove (const REAL mutationAmplitude, const RefParType *type=gpRefParTypeObjCryst)
	Make a random move of the current configuration. More...

virtual REAL	GetLogLikelihood () const
	Get -log(likelihood) of the current configuration for the object. More...

virtual unsigned int	GetNbLSQFunction () const
	Number of LSQ functions.

virtual const CrystVector_REAL &	GetLSQCalc (const unsigned int) const
	Get the current calculated value for the LSQ function.

virtual const CrystVector_REAL &	GetLSQObs (const unsigned int) const
	Get the observed values for the LSQ function.

virtual const CrystVector_REAL &	GetLSQWeight (const unsigned int) const
	Get the weight values for the LSQ function.

virtual std::map< RefinablePar *, CrystVector_REAL > &	GetLSQ_FullDeriv (const unsigned int, std::set< RefinablePar * > &vPar)
	Get the first derivative for the LSQ function for each parameter supplied in a list. More...

virtual void	XMLOutput (ostream &os, int indent=0) const
	Output to stream in well-formed XML. More...

virtual void	XMLInput (istream &is, const XMLCrystTag &tag)
	Input From stream. More...

virtual const Radiation &	GetRadiation () const
	Get the radiation object for this data.

Radiation &	GetRadiation ()

virtual void	SetRadiationType (const RadiationType radiation)
	Set : neutron or x-ray experiment ? Wavelength ?

void	SetWavelength (const REAL)
	Set the (monochromatic) wavelength of the beam.

void	SetWavelength (const string &XRayTubeElementName, const REAL alpha2Alpha2ratio=0.5)
	\ brief Set X-Ray tube radiation. More...

void	SetEnergy (const REAL)
	Set the (monochromatic) energy of the beam.

Public Member Functions inherited from ObjCryst::ScatteringData
	ScatteringData (const ScatteringData &old)

virtual void	SetHKL (const CrystVector_REAL &h, const CrystVector_REAL &k, const CrystVector_REAL &l)
	input H,K,L More...

virtual void	GenHKLFullSpace2 (const REAL maxsithsl, const bool unique=false)
	Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value. More...

virtual void	GenHKLFullSpace (const REAL maxTheta, const bool unique=false)
	Generate a list of h,k,l to describe a full reciprocal space, up to a given maximum theta value. More...

RadiationType	GetRadiationType () const
	Neutron or x-ray experiment ? Wavelength ?

virtual void	SetCrystal (Crystal &crystal)
	Set the crystal for this experiment. More...

const Crystal &	GetCrystal () const
	Const access to the data's crystal.

Crystal &	GetCrystal ()
	Access to the data's crystal.

bool	HasCrystal () const
	Has a Crystal structure associated yet ?

long	GetNbRefl () const
	Return the number of reflections in this experiment.

const CrystVector_REAL &	GetH () const
	Return the 1D array of H coordinates for all reflections.

const CrystVector_REAL &	GetK () const
	Return the 1D array of K coordinates for all reflections.

const CrystVector_REAL &	GetL () const
	Return the 1D array of L coordinates for all reflections.

const CrystVector_REAL &	GetH2Pi () const
	Return the 1D array of H coordinates for all reflections, multiplied by 2*pi. More...

const CrystVector_REAL &	GetK2Pi () const
	Return the 1D array of K coordinates for all reflections, multiplied by 2*pi. More...

const CrystVector_REAL &	GetL2Pi () const
	Return the 1D array of L coordinates for all reflections, multiplied by 2*pi. More...

const CrystVector_REAL &	GetReflX () const
	Return the 1D array of orthonormal x coordinates for all reflections (recipr. space)

const CrystVector_REAL &	GetReflY () const
	Return the 1D array of orthonormal y coordinates for all reflections (recipr. space)

const CrystVector_REAL &	GetReflZ () const
	Return the 1D array of orthonormal z coordinates for all reflections (recipr. space)

const CrystVector_REAL &	GetSinThetaOverLambda () const
	Return an array with $\frac{sin(\theta)}{\lambda} = \frac{1}{2d_{hkl}}$ for all reflections.

const CrystVector_REAL &	GetTheta () const
	Return an array with theta values for all reflections.

const RefinableObjClock &	GetClockTheta () const
	Clock the last time the sin(theta)/lambda and theta arrays were re-computed.

const CrystVector_REAL &	GetFhklCalcSq () const
	Returns the Array of calculated \|F(hkl)\|^2 for all reflections.

std::map< RefinablePar *, CrystVector_REAL > &	GetFhklCalcSq_FullDeriv (std::set< RefinablePar * > &vPar)

const CrystVector_REAL &	GetFhklCalcReal () const
	Access to real part of F(hkl)calc.

const CrystVector_REAL &	GetFhklCalcImag () const
	Access to imaginary part of F(hkl)calc.

const CrystVector_REAL &	GetFhklObsSq () const
	Returns the Array of observed \|F(hkl)\|^2 for all reflections.

const map< const ScatteringPower *, CrystVector_REAL > &	GetScatteringFactor () const
	Scattering factors for each ScatteringPower, as vectors with NbRefl elements.

CrystVector_REAL	GetWavelength () const
	wavelength of the experiment (in Angstroems)

void	SetIsIgnoringImagScattFact (const bool b)
	If true, then the imaginary part of the scattering factor is ignored during Structure factor computation. More...

bool	IsIgnoringImagScattFact () const
	If true, then the imaginary part of the scattering factor is ignored during Structure factor computation. More...

virtual void	PrintFhklCalc (ostream &os=cout) const
	Print H, K, L F^2 Re(F) Im(F) theta sin(theta)/lambda for all reflections. More...

virtual void	PrintFhklCalcDetail (ostream &os=cout) const
	Print H, K, L sin(theta)/lambda theta F^2 Re(F) Im(F) [Re(F) Im(F)]_i, where [Re(F) Im(F)]_i are the real and imaginary contribution of the different scattering powers to the overall structure factor.

virtual void	BeginOptimization (const bool allowApproximations=false, const bool enableRestraints=false)
	This should be called by any optimization class at the begining of an optimization. More...

virtual void	EndOptimization ()
	This should be called by any optimization class at the end of an optimization. More...

virtual void	SetApproximationFlag (const bool allow)
	Enable or disable numerical approximations. More...

virtual void	SetMaxSinThetaOvLambda (const REAL max)
	Set the maximum value for sin(theta)/lambda. More...

REAL	GetMaxSinThetaOvLambda () const
	Get the maximum value for sin(theta)/lambda.

virtual long	GetNbReflBelowMaxSinThetaOvLambda () const
	Recalc, and get the number of reflections which should be actually used, due to the maximuml sin(theta)/lambda value set. More...

const RefinableObjClock &	GetClockNbReflBelowMaxSinThetaOvLambda () const
	Clock the last time the number of reflections used was changed.

Public Member Functions inherited from ObjCryst::RefinableObj
	RefinableObj ()
	Constructor.

	RefinableObj (const bool internalUseOnly)
	Constructor. More...

	RefinableObj (const RefinableObj &old)
	Defined not implemented... More...

virtual	~RefinableObj ()
	Destructor.

virtual const string &	GetName () const
	Name of the object.

virtual void	SetName (const string &name)
	Name of the object.

void	operator= (const RefinableObj &old)
	Defined not implemented... More...

void	PrepareForRefinement () const
	Find which parameters are used and not fixed, for a refinement /optimization. More...

void	FixAllPar ()
	Fix All parameters.

void	UnFixAllPar ()
	UnFix All parameters.

void	SetParIsFixed (const long parIndex, const bool fix)
	Fix/un-fix one parameter from its #.

void	SetParIsFixed (const string &parName, const bool fix)
	Fix/un-fix one parameter from its name.

void	SetParIsFixed (const RefParType *type, const bool fix)
	Fix/un-fix one family of parameters.

void	SetParIsUsed (const string &parName, const bool use)
	Set whether a parameter is used.

void	SetParIsUsed (const RefParType *type, const bool use)
	Set whether a family of parameters is used.

long	GetNbPar () const
	Total number of refinable parameter in the object. More...

long	GetNbParNotFixed () const
	Total number of non-fixed parameters. Is initialized by PrepareForRefinement()

RefinablePar &	GetPar (const long i)
	Access all parameters in the order they were inputted.

const RefinablePar &	GetPar (const long i) const
	Access all parameters in the order they were inputted.

RefinablePar &	GetPar (const string &name)
	Access all parameters from their name.

const RefinablePar &	GetPar (const string &name) const
	Access all parameters from their name.

RefinablePar &	GetPar (const REAL *)
	Access parameter from its adress.

const RefinablePar &	GetPar (const REAL *) const
	Access parameter from its adress.

RefinablePar &	GetParNotFixed (const long i)
	Access all parameters in the order they were inputted, skipping fixed parameters. More...

const RefinablePar &	GetParNotFixed (const long i) const
	Access all parameters in the order they were inputed, skipping fixed parameters. More...

void	AddPar (const RefinablePar &newRefPar)
	Add a refinable parameter. More...

void	AddPar (RefinablePar *newRefPar)
	Add a refinable parameter. More...

void	AddPar (RefinableObj &newRefParList, const bool copyParam=false)
	Add all the parameters in another RefinableObj. More...

vector< RefinablePar * >::iterator	RemovePar (RefinablePar *refPar)
	Remove a refinable parameter. More...

virtual void	Print () const

unsigned long	CreateParamSet (const string name="") const
	Save the current set of refined values in a new set. More...

void	ClearParamSet (const unsigned long id) const
	Erase the param set with the given id, releasing memory.

void	SaveParamSet (const unsigned long id) const
	Save the current set of refined values over a previously-created set of saved values. More...

void	RestoreParamSet (const unsigned long id)
	Restore a saved set of values. More...

const CrystVector_REAL &	GetParamSet (const unsigned long setId) const
	Access one save refpar set. More...

CrystVector_REAL &	GetParamSet (const unsigned long setId)
	Access one save refpar set. More...

REAL	GetParamSet_ParNotFixedHumanValue (const unsigned long setId, const long parNumber) const
	Access the (human) value of one refined parameter in a saved set of parameters. More...

const void	EraseAllParamSet ()
	Erase all saved refpar sets. More...

const string &	GetParamSetName (const unsigned long setId) const
	Get the name associated to a refpar set. More...

void	SetLimitsAbsolute (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, giving absolute new limits.

void	SetLimitsAbsolute (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, giving absolute new limits.

void	SetLimitsRelative (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max) Thus min should logically be <0 and max >0. More...

void	SetLimitsRelative (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, giving relative new limits (eg giving -.1 and +.1 will set new limits at the current value + min and current value + max). More...

void	SetLimitsProportional (const string &parName, const REAL min, const REAL max)
	Change the limits for a given parameter, proportionnaly to the current value. More...

void	SetLimitsProportional (const RefParType *type, const REAL min, const REAL max)
	Change the limits for a category of parameters, proportionnaly to their current value. More...

void	SetGlobalOptimStep (const RefParType *type, const REAL step)
	Change the maximum step to use during Global Optimization algorithms.

ObjRegistry< RefinableObj > &	GetSubObjRegistry ()
	Access to the registry of RefinableObj used by this object.

const ObjRegistry< RefinableObj > &	GetSubObjRegistry () const
	Access to the registry of RefinableObj used by this object.

virtual void	RegisterClient (RefinableObj &) const
	Register a new object using this object. More...

virtual void	DeRegisterClient (RefinableObj &) const
	Deregister an object (which not any more) using this object.

virtual const ObjRegistry < RefinableObj > &	GetClientRegistry () const
	Get the list of clients.

virtual ObjRegistry < RefinableObj > &	GetClientRegistry ()
	Get the list of clients.

bool	IsBeingRefined () const
	Is the object being refined ? (Can be refined by one algorithm at a time only.)

virtual void	RandomizeConfiguration ()
	Randomize Configuration (before a global optimization). More...

void	BeginGlobalOptRandomMove ()
	Raise a flag, to be sure not to make a random change more than once in each RefinableObj. More...

virtual const CrystVector_REAL &	GetLSQDeriv (const unsigned int, RefinablePar &)
	Get the first derivative values for the LSQ function, for a given parameter. More...

void	ResetParList ()
	Re-init the list of refinable parameters, removing all parameters. More...

virtual void	UpdateDisplay () const
	If there is an interface, this should be automatically be called each time there is a 'new, significant' configuration to report. More...

unsigned int	GetNbOption () const
	Number of Options for this object.

RefObjOpt &	GetOption (const unsigned int i)
	Access to the options.

const RefObjOpt &	GetOption (const unsigned int i) const
	const access to the options

virtual void	GetGeneGroup (const RefinableObj &obj, CrystVector_uint &groupIndex, unsigned int &firstGroup) const
	Get the gene group assigned to each parameter. More...

void	SetDeleteRefParInDestructor (const bool b)
	Set this object not to delete its list of parameters when destroyed. More...

const RefinableObjClock &	GetRefParListClock () const
	What was the last time a RefinablePar was added/removed ? More...

virtual REAL	GetRestraintCost () const
	Get the restraint cost (overall penalty of all restraints) More...

void	AddRestraint (Restraint *pNewRestraint)
	Add a new restraint. More...

vector< Restraint * >::iterator	RemoveRestraint (Restraint *pRestraint)
	Remove a restraint from the list of known restraints. More...

virtual void	TagNewBestConfig () const
	During a global optimization, tells the object that the current config is the latest "best" config. More...

const RefinableObjClock &	GetClockMaster () const
	This clocks records any change in the object. See refinableObj::mClockMaster.

Private Member Functions
virtual void	InitRefParList ()

void	CalcIcalc () const
	Calc intensities.

void	CalcIcalc_FullDeriv (std::set< RefinablePar * > &vPar)

virtual CrystVector_long	SortReflectionBySinThetaOverLambda (const REAL maxTheta=-1.)

void	InitOptions ()
	Init options (currently only twinning).

void	PrepareTwinningCalc () const
	Determine the index of reflections to be summed because of twinning (GroupOption==1) The reflections must have been sorted by increasing theta beforehand. More...

Private Attributes
bool	mHasObservedData
	Are there observed intensities ?

CrystVector_REAL	mObsIntensity
	Observed intensity (after ABS and LP corrections) More...

CrystVector_REAL	mObsSigma
	Sigma for observed intensities (either individual reflections or spectrum)

CrystVector_REAL	mWeight
	weight for computing R-Factor, for each observed value.

CrystVector_REAL	mCalcIntensity
	Calculated intensities.

std::map< RefinablePar *, CrystVector_REAL >	mCalcIntensity_FullDeriv

REAL	mScaleFactor
	Scale factor. More...

REAL	mChi2
	Chi^2.

RefinableObjClock	mClockIcalc
	Last time Icalc was computed.

RefinableObjClock	mClockScaleFactor
	Last modification of the scale factor.

RefinableObjClock	mClockChi2
	Clock the last time Chi^2 was computed.

RefObjOpt	mGroupOption
	Option for the type of grouping (0:no, 1:by theta values (twinning), 2:user-supplied groups)

CrystVector_REAL	mGroupIobs
	The observed intensities summed on all reflections that are (or could be) overlapped dur to a twinning.

CrystVector_REAL	mGroupSigma
	The uncertainty on observed grouped intensities.

CrystVector_REAL	mGroupIcalc
	The calculated intensities summed on all reflections that are grouped.

std::map< RefinablePar *, CrystVector_REAL >	mGroupIcalc_FullDeriv

CrystVector_REAL	mGroupWeight
	The weight on each reflection sum in case of grouped reflections. More...

CrystVector_long	mGroupIndex
	The index of reflections which need to be summed. More...

long	mNbGroup
	Number of groups.

long	mNbGroupUsed
	Number of groups below max[sin(theta)/lambda].

RefinableObjClock	mClockPrepareTwinningCorr
	Clock for twinning, when the preparation of twinning correction was last made.

Radiation	mRadiation

Additional Inherited Members
Protected Member Functions inherited from ObjCryst::ScatteringData
virtual void	PrepareHKLarrays ()

CrystVector_long	EliminateExtinctReflections ()

virtual void	CalcSinThetaLambda () const

REAL	CalcSinThetaLambda (REAL h, REAL k, REAL l) const
	Calculate sin(theta)/lambda for a single reflection.

virtual const CrystMatrix_REAL &	GetBMatrix () const
	Get access to the B matrix used to compute reflection positions. More...

void	CalcScattFactor () const

void	CalcTemperatureFactor () const

virtual void	CalcResonantScattFactor () const

void	CalcGlobalTemperatureFactor () const
	Compute the overall temperature factor affecting all reflections.

void	CalcStructFactor () const
	Compute the overall structure factor (real and imaginary part). More...

void	CalcStructFactor_FullDeriv (std::set< RefinablePar * > &vPar)

void	CalcGeomStructFactor () const
	Compute the 'Geometrical Structure Factor' for each ScatteringPower of the Crystal. More...

void	CalcGeomStructFactor_FullDeriv (std::set< RefinablePar * > &vPar)

void	CalcLuzzatiFactor () const
	Calculate the Luzzati factor associated to each ScatteringPower and each reflection, for maximum likelihood optimization.

void	CalcStructFactVariance () const
	Calculate the variance associated to the calculated structure factor. More...

Protected Member Functions inherited from ObjCryst::RefinableObj
long	FindPar (const string &name) const
	Find a refinable parameter with a given name.

long	FindPar (const REAL *) const
	Find a refinable parameter from the adress of its value.

void	AddSubRefObj (RefinableObj &)

void	RemoveSubRefObj (RefinableObj &)

void	AddOption (RefObjOpt *opt)

virtual void	Prepare ()

map< unsigned long, pair < CrystVector_REAL, string > >::iterator	FindParamSet (unsigned long id) const
	Find a parameter set with a given id (and check if it is there)

Protected Attributes inherited from ObjCryst::ScatteringData
long	mNbRefl
	Number of H,K,L reflections.

CrystVector_REAL	mH
	H,K,L coordinates.

CrystVector_REAL	mK

CrystVector_REAL	mL

CrystVector_long	mIntH
	H,K,L integer coordinates.

CrystVector_long	mIntK

CrystVector_long	mIntL

CrystVector_REAL	mH2Pi
	H,K,L coordinates, multiplied by 2PI.

CrystVector_REAL	mK2Pi

CrystVector_REAL	mL2Pi

CrystVector_REAL	mX
	reflection coordinates in an orthonormal base

CrystVector_REAL	mY

CrystVector_REAL	mZ

CrystVector_int	mMultiplicity
	Multiplicity for each reflections (mostly for powder diffraction)

CrystVector_int	mExpectedIntensityFactor
	Expected intensity factor for all reflections. More...

CrystVector_REAL	mFhklCalcReal
	real &imaginary parts of F(HKL)calc

CrystVector_REAL	mFhklCalcImag

std::map< RefinablePar *, CrystVector_REAL >	mFhklCalcReal_FullDeriv

std::map< RefinablePar *, CrystVector_REAL >	mFhklCalcImag_FullDeriv

CrystVector_REAL	mFhklCalcSq
	F(HKL)^2 calc for each reflection.

std::map< RefinablePar *, CrystVector_REAL >	mFhklCalcSq_FullDeriv

Crystal *	mpCrystal
	Pointer to the crystal corresponding to this experiment. More...

REAL	mGlobalBiso
	Global Biso, affecting the overall structure factor for all reflections (but not the structure factors of individual atoms or type of atomes).

CrystVector_REAL	mGlobalTemperatureFactor
	Global Biso factor.

bool	mUseFastLessPreciseFunc
	Use faster, but less precise, approximations for functions? (integer approximations to compute sin and cos in structure factors, and also to compute interatomic distances). More...

CrystVector_REAL	mSinThetaLambda
	$\frac{sin(\theta)}{\lambda} = \frac{1}{2d_{hkl}}$ for the crystal and the reflections in ReciprSpace

CrystVector_REAL	mTheta
	theta for the crystal and the HKL in ReciprSpace (in radians)

map< const ScatteringPower *, REAL >	mvFprime
	Anomalous X-Ray scattering term f' and f" are stored here for each ScatteringPower We store here only a value. More...

map< const ScatteringPower *, REAL >	mvFsecond

map< const ScatteringPower *, CrystVector_REAL >	mvTemperatureFactor
	Thermic factors for each ScatteringPower, as vectors with NbRefl elements.

map< const ScatteringPower *, CrystVector_REAL >	mvScatteringFactor
	Scattering factors for each ScatteringPower, as vectors with NbRefl elements.

map< const ScatteringPower *, CrystVector_REAL >	mvRealGeomSF
	Geometrical Structure factor for each ScatteringPower, as vectors with NbRefl elements.

map< const ScatteringPower *, CrystVector_REAL >	mvImagGeomSF

map< RefinablePar , map < const ScatteringPower , CrystVector_REAL > >	mvRealGeomSF_FullDeriv

map< RefinablePar , map < const ScatteringPower , CrystVector_REAL > >	mvImagGeomSF_FullDeriv

RefinableObjClock	mClockHKL
	Clock for the list of hkl.

RefinableObjClock	mClockStructFactor
	Clock for the structure factor.

RefinableObjClock	mClockStructFactorSq
	Clock for the square modulus of the structure factor.

RefinableObjClock	mClockTheta
	Clock the last time theta was computed.

RefinableObjClock	mClockScattFactor
	Clock the last time scattering factors were computed.

RefinableObjClock	mClockScattFactorResonant
	Clock the last time resonant scattering factors were computed.

RefinableObjClock	mClockGeomStructFact
	Clock the last time the geometrical structure factors were computed.

RefinableObjClock	mClockThermicFact
	Clock the last time temperature factors were computed.

RefinableObjClock	mClockGlobalBiso
	last time the global Biso factor was modified

RefinableObjClock	mClockGlobalTemperatureFact
	last time the global temperature factor was computed

bool	mIgnoreImagScattFact
	Ignore imaginary part of scattering factor. More...

REAL	mMaxSinThetaOvLambda
	Maximum sin(theta)/lambda for all calculations (10 by default). More...

long	mNbReflUsed
	Number of reflections which are below the max. More...

RefinableObjClock	mClockNbReflUsed
	Clock recording the last time the number of reflections used has increased.

map< const ScatteringPower *, CrystVector_REAL >	mvLuzzatiFactor
	The Luzzati 'D' factor for each scattering power and each reflection.

CrystVector_REAL	mFhklCalcVariance
	The variance on all calculated structure factors, taking into account the positionnal errors and the expected intensity factor. More...

RefinableObjClock	mClockLuzzatiFactor

RefinableObjClock	mClockFhklCalcVariance

CrystVector_REAL	mFhklObsSq
	Observed squared structure factors (zero-sized if none)

RefinableObjClock	mClockFhklObsSq
	Last time observed squared structure factors were altered.

Protected Attributes inherited from ObjCryst::RefinableObj
string	mName
	Name for this RefinableObject. Should be unique, at least in the same scope.+.

vector< RefinablePar * >	mvpRefPar
	Vector of pointers to the refinable parameters.

vector< Restraint * >	mvpRestraint
	Vector of pointers to the restraints for this object. More...

map< unsigned long, pair < CrystVector_REAL, string > >	mvpSavedValuesSet
	Map of (index,pointers to arrays) used to save sets of values for all parameters. More...

long	mNbRefParNotFixed
	Total of not-fixed parameters.

CrystVector_long	mRefparNotFixedIndex
	Index of not-fixed parameters.

int	mOptimizationDepth
	Is the object being refined or optimized ? if mOptimizationDepth=0, no optimization is taking place. More...

ObjRegistry< RefinableObj >	mSubObjRegistry
	Registry of RefinableObject needed for this object (owned by this object or not)

ObjRegistry< RefinableObj >	mClientObjRegistry
	Registry of RefinableObject using this object. More...

ObjRegistry< RefObjOpt >	mOptionRegistry
	List of options for this object. More...

bool	mDeleteRefParInDestructor
	If true (the default), then all RefinablePar will be deleted when the the object is deleted. More...

RefinableObjClock	mRefParListClock
	Last time the RefinableParList was modified (a parameter added or removed).

bool	mRandomMoveIsDone

CrystVector_REAL	mLSQDeriv
	Temporary array used to return derivative values of the LSQ function for given parameters. More...

std::map< unsigned int, std::map< RefinablePar *, CrystVector_REAL > >	mLSQ_FullDeriv
	Temporary map to return the derivative of the LSQ function versus a list of parameters. More...

RefinableObjClock	mClockMaster
	Master clock, which is changed whenever the object has been altered. More...

Detailed Description

DiffractionData object for Single Crystal analysis.

Currently this handles only in the simplest way single crystal dat: ie only data which has been completely corrected for Lorentz/Polarization and absorption.

What needs to be developped: define the geometry of the experiment (incident and emerging angles), the polarization of the beam, etc...

Definition at line 50 of file DiffractionDataSingleCrystal.h.

Constructor & Destructor Documentation

ObjCryst::DiffractionDataSingleCrystal::DiffractionDataSingleCrystal ( const bool regist = true )

Default constructor.

Parameters

regist if false, do not add to the global registry of single crystal data or refinable objects - this is only useful for data to be used internally only.

Deprecated:: Use the constructor passing a crystal structure instead.

Definition at line 57 of file DiffractionDataSingleCrystal.cpp.

ObjCryst::DiffractionDataSingleCrystal::DiffractionDataSingleCrystal	(	Crystal &	cryst,
		const bool	regist = `true`
	)

Constructor, with an assigned crystal structure.

Parameters

regist if false, do not add to the global registry of single crystal data or refinable objects - this is only useful for data to be used internally only.

Definition at line 68 of file DiffractionDataSingleCrystal.cpp.

Member Function Documentation

void ObjCryst::DiffractionDataSingleCrystal::FitScaleFactorForR ( ) const

virtual

Compute the best scale factor minimising R.

The computed scale factor is immediatly applied to Icalc

Definition at line 855 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::FitScaleFactorForRw ( ) const

virtual

Compute the best scale factor minimising Rw.

The computed scale factor is immediatly applied to Icalc

Definition at line 810 of file DiffractionDataSingleCrystal.cpp.

REAL ObjCryst::DiffractionDataSingleCrystal::GetBestRFactor ( ) const

virtual

Compute the best scale factor to minimize R, apply this scale factor and return the R value obtained.

Definition at line 897 of file DiffractionDataSingleCrystal.cpp.

REAL ObjCryst::DiffractionDataSingleCrystal::GetChi2 ( ) const

virtual

Return conventionnal Chi^2.

Returns: $\chi^2 = \sum_i w_i \left(I_i^{obs}-I_i^{calc} \right)^2$

Definition at line 733 of file DiffractionDataSingleCrystal.cpp.

const string & ObjCryst::DiffractionDataSingleCrystal::GetClassName ( ) const

virtual

Name for this class ("RefinableObj", "Crystal",...).

This is only useful to distinguish different classes when picking up objects from the RefinableObj Global Registry

Reimplemented from ObjCryst::RefinableObj.

Definition at line 116 of file DiffractionDataSingleCrystal.cpp.

const CrystVector_REAL & ObjCryst::DiffractionDataSingleCrystal::GetIcalc ( ) const

returns the calculated diffracted intensity.

This is an array of calculated intensities for each reflections in the single crystal case, and the array with the full powder powder profile for powder diffraction.

Definition at line 166 of file DiffractionDataSingleCrystal.cpp.

std::map< RefinablePar *, CrystVector_REAL > & ObjCryst::DiffractionDataSingleCrystal::GetIcalc_FullDeriv ( std::set< RefinablePar * > & vPar )

Todo:

Definition at line 172 of file DiffractionDataSingleCrystal.cpp.

REAL ObjCryst::DiffractionDataSingleCrystal::GetLogLikelihood ( ) const

virtual

Get -log(likelihood) of the current configuration for the object.

By default (no likelihood evaluation available), this is equal to 0.

This call should not be recursive, it is the task of the algorithm to get the sum of likelihoods for all objects invlolved.

Note: contrary to the old "Cost Function" approach, with log(Likelihood) there is no 'choice' of cost function, so that it is the task of the object to give the optimized likelihood (possibly with user options).

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1013 of file DiffractionDataSingleCrystal.cpp.

std::map< RefinablePar *, CrystVector_REAL > & ObjCryst::DiffractionDataSingleCrystal::GetLSQ_FullDeriv	(	const unsigned int	n,
		std::set< RefinablePar * > &	vPar
	)

virtual

Get the first derivative for the LSQ function for each parameter supplied in a list.

Returns: : a map, with a RefinablePar pointer as key, and as value the corresponding derivative vector. Note that the value of the map for the NULL key is the current value for the LSQ function, which is also returned. The map will include derivatives only for parameters which have been supplied in vPar - but if a parameter is listed in vPar and has a null derivative, the returned vecor will be empty.

Warning: : currently in development, to provide faster, analytic derivatives

Note: :ideally, this function should be const - but since numerical derivatives may be used before all analytical formulas are entered, a non-const version is required.

Todo:

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1042 of file DiffractionDataSingleCrystal.cpp.

REAL ObjCryst::DiffractionDataSingleCrystal::GetR ( ) const

virtual

Return the Crystal R-factor (unweighted)

Returns: $R= \sqrt {\frac{\sum_i \left( I_i^{obs}-I_i^{calc} \right)^2} {\sum_i (I_i^{obs})^2} }$

Definition at line 694 of file DiffractionDataSingleCrystal.cpp.

REAL ObjCryst::DiffractionDataSingleCrystal::GetRw ( ) const

virtual

Return the Crystal R-factor (weighted)

Returns: $R_{w}= \sqrt {\frac{\sum_i w_i\left( I_i^{obs}-I_i^{calc} \right)^2} {\sum_i w_i (I_i^{obs})^2} }$

Definition at line 654 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::GlobalOptRandomMove	(	const REAL	mutationAmplitude,
		const RefParType *	type = `gpRefParTypeObjCryst`
	)

virtual

Make a random move of the current configuration.

This is for global optimization algorithms. the moves for each parameter are less than their global optimization step, multiplied by the mutation amplitude.

Warning: : this makes a random move for the parameter declared for this object, and it is the duty of the object to decide whether the included objects should be moved and how. (eg an algorithm should only call for a move with the top object, and this object decides how he and his sub-objects moves). By default (RefinableObj implementation) all included objects are moved recursively.

RefinableObj::

Parameters

mutationAmplitude	multiplier for the maximum move amplitude, for all parameters
type	restrain the change exclusively to parameters of a given type (same type or descendant from this RefParType).

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1006 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::ImportCIF ( const string & fileName )

Import diffraction data from a CIF file.

The file is assumed to correspond to a single crystal diffraction file.

Parameters

fileName The name of the data file.

Definition at line 438 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::ImportHklIobs	(	const string &	fileName,
		const long	nbRefl,
		const int	skipLines = `0`
	)

Import h,k,l,I from a file.

The file is assumed to correspond to a single crystal diffraction file.

Parameters

fileName	The name of the data file. This file should be formatted with H,k,l, Iobs separated by spaces.
nbRefl	The number of reflections to extract.
skipLines	The number of lines to skip at the beginning of the file.

Definition at line 231 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::ImportHklIobsGroup	(	const string &	fileName,
		const unsigned int	skipLines = `0`
	)

Import h,k,l and grouped intensities from a file.

The file is assumed to correspond to a single crystal diffraction file.

Parameters

fileName	The name of the data file. This file should be formatted with H,k,l, Iobs separated by spaces.
skipLines	The number of lines to skip at the beginning of the file.

File format (the reflection which has an intensity entry marks the end of the group) h k l Igroup -2 4 2 -2 -4 2 100.4 2 -4 1 2 4 1 193.2 ...

Definition at line 539 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::ImportHklIobsSigma	(	const string &	fileName,
		const long	nbRefl,
		const int	skipLines = `0`
	)

Import h,k,l,I,Sigma from a file.

The file is assumed to correspond to a single crystal diffraction file.

Parameters

fileName	The name of the data file. This file should be formatted with H,k,l, Iobs and Sigma separated by spaces.
nbRefl	The number of reflections to extract.
skipLines	The number of lines to skip at the beginning of the file.

Definition at line 294 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::ImportHklIobsSigmaJanaM91 ( const string & fileName )

Import h,k,l,I,Sigma from a Jana98 '*.m91' file.

The file is assumed to correspond to a single crystal diffraction file.

Parameters

fileName The name of the data file.

Definition at line 458 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::ImportShelxHKLF4 ( const string & fileName )

Import h,k,l,I,Sigma from a file using shelx HKLF 4 format.

The file is assumed to correspond to a single crystal diffraction file.This file should be formatted with H,k,l, Iobs and Sigma using a strict formatting 3I4+2F8, and the last line should contain 0 0 0 for hkl values.

Parameters

fileName The name of the data file.

Definition at line 359 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::PrepareTwinningCalc ( ) const

private

Determine the index of reflections to be summed because of twinning (GroupOption==1) The reflections must have been sorted by increasing theta beforehand.

Definition at line 1305 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::PrintObsData ( ) const

virtual

Print H, K, L Iobs sigma for all reflections.

Definition at line 929 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::SaveHKLIobsIcalc ( const string & filename = "hklIobsIcalc.out" )

Save H,K,L Iobs Icalc to a file, text format, 3 columns theta Iobs Icalc.

If Iobs is missing, the column is omitted.

Definition at line 979 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::SetHklIobs	(	const CrystVector_long &	h,
		const CrystVector_long &	k,
		const CrystVector_long &	l,
		const CrystVector_REAL &	iObs,
		const CrystVector_REAL &	sigma
	)

input H,K,L, Iobs and Sigma

Parameters

h,k,l	REAL arrays (vectors with NbRefl elements -same size) with the h, k and l coordinates of all reflections.
iobs,sigma	REAL arrays (vectors with NbRefl elements -same size) with the Observed intensity and sigma for all reflections.

Definition at line 122 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::SetSigmaToSqrtIobs ( )

virtual

Set sigma for all observed intensities to sqrt(obs)

Definition at line 905 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::SetWavelength	(	const string &	XRayTubeElementName,
		const REAL	alpha2Alpha2ratio = `0.5`
	)

\ brief Set X-Ray tube radiation.

Parameters

XRayTubeElementName	: name of the anticathode element name. Known ones are Cr, Fe, Cu, Mo, Ag.
alpha2Alpha2ratio	Kalpha2/Kalpha1 ratio (0.5 by default)

the average wavelength is calculated using the alpha2/alpha1 weight. All structure factors computation are made using the average wavelength, and for powder diffraction, profiles are output at the alpha1 and alpha2 ratio for the calculated pattern.

NOTE : if the name of the wavelength is generic (eg"Cu"), then the program considers that there are both Alpha1 and Alpha2, and thus automatically changes the WavelengthType to WAVELENGTH_ALPHA12. If instead either alpha1 or alpha2 (eg "CuA1") is asked for, the WavelengthType is set to WAVELENGTH_MONOCHROMATIC. In both cases, the radiation type is set to X-Ray.

Definition at line 1077 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::SetWeightToInvSigma2	(	const REAL	minRelatSigma = `1e-4`,
		const REAL	minIobsSigmaRatio = `0`
	)

virtual

Set the weight for all observed intensities to 1/sigma^2.

For sigmas which are smaller than minRelatSigma times the max value of sigma, the output weight is set to 0.

For reflections where the intensity is below minIobsSigmaRatio*sigma, the weight is set to zero so that this reflection is ignored.

Definition at line 912 of file DiffractionDataSingleCrystal.cpp.

CrystVector_long ObjCryst::DiffractionDataSingleCrystal::SortReflectionBySinThetaOverLambda ( const REAL maxSTOL = -1. )

privatevirtual

sort reflections by theta values (also get rid of [0,0,0] if present) If maxSTOL >0, then only reflections where sin(theta)/lambda<maxSTOL are kept

Returns: an array with the subscript of the kept reflections (for inherited classes)

Reimplemented from ObjCryst::ScatteringData.

Definition at line 1168 of file DiffractionDataSingleCrystal.cpp.

void ObjCryst::DiffractionDataSingleCrystal::XMLInput	(	istream &	is,
		const XMLCrystTag &	tag
	)

virtual

Input From stream.

Todo:: Add an bool XMLInputTag(is,tag) function to recognize all the tags from the stream. So that each inherited class can use the XMLInputTag function from its parent (ie take advantage of inheritance). The children class would first try to interpret the tag, then if unsuccessful would pass it to its parent (thus allowing overloading), etc...

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1280 of file ObjCryst/IO.cpp.

void ObjCryst::DiffractionDataSingleCrystal::XMLOutput	(	ostream &	os,
		int	indent = `0`
	)		const

virtual

Output to stream in well-formed XML.

Todo:: Use inheritance.. as for XMLInputTag()...

Reimplemented from ObjCryst::RefinableObj.

Definition at line 1180 of file ObjCryst/IO.cpp.

Member Data Documentation

CrystVector_long ObjCryst::DiffractionDataSingleCrystal::mGroupIndex

mutableprivate

The index of reflections which need to be summed.

They must have been sorted by increasing theta values. Each entry (the reflection index) marks the beginning of a new batch of reflections to be summed.

Here only the groups of reflections are roughly sorted by sin(theta)/lambda. It is assumed, howver, that grouped reflections are of approximately the same d_hkl. After ScatteringData::GetNbReflBelowMaxSinThetaOvLambda(), the number of groups for which all reflections are below the limit are taken into account for the statistics.

Note that DiffractionDataSingleCrystal::SortReflectionBySinThetaOverLambda() is called (i.e. immediately after importing the reflections)

Definition at line 356 of file DiffractionDataSingleCrystal.h.

CrystVector_REAL ObjCryst::DiffractionDataSingleCrystal::mGroupWeight

mutableprivate

The weight on each reflection sum in case of grouped reflections.

The sum is the inverse of the sum of all sigma^2

Definition at line 342 of file DiffractionDataSingleCrystal.h.

CrystVector_REAL ObjCryst::DiffractionDataSingleCrystal::mObsIntensity

private

Observed intensity (after ABS and LP corrections)

In the single crystal case, this is a list of intensity corresponding to (h,k,l). For a powder sample, this is a list of all peaks intensities.

Definition at line 308 of file DiffractionDataSingleCrystal.h.